Éditeur(s) : HAL CCSD Linnean Society of London
Résumé : International audience
Although migratory pelagic fishes generally exhibit little geographic differentiation across oceans, as expected from their life-history (broadcast spawning, pelagic larval life, swimming ability of adults) and the assumed homogeneity of the pelagic habitat, exceptions to the rule deserve scrutiny. One such exception is the narrow-barred Spanish mackerel (Scomberomorus commerson), where strong genetic heterogeneity at the regional scale has been previously reported. We investigated the genetic composition of S. commerson across the Indo-West Pacific range using control-region sequences (including previously published datasets), cytochrome-b gene partial sequences, and eight microsatellite loci, to further explore its phylogeographic structure. All haplotypes sampled from the Indo-Malay-Papua archipelago (IMPA) and the southwestern Pacific coalesced into a clade (Clade II) that was deeply separated (14.5% nucleotide divergence) from a clade grouping all haplotypes from the Persian Gulf and Oman Sea (Clade I). Such a high level of genetic divergence suggested the occurrence of two sister-species. Further phylogeographic partition was evident between the western IMPA and the regions sampled east and south of it, i.e. northern Australia, West Papua, and the Coral Sea. Strong allele-frequency differences were found between local populations in the southwestern Pacific, both at the mitochondrial locus (ΦST=0.282-0.609) and at microsatellite loci (^θ=0.202-0.313). Clade II consisted of four deeply divergent subclades (9.0-11.8% nucleotide divergence for the control region; 0.3-2.5% divergence at the cytochrome b locus). Mitochondrial sub-clades within Clade II generally had narrow geographic distribution, demonstrating further genetic isolation. However, one particular haplogroup within Clade II was present throughout the central Indo-West Pacific; that haplogroup was found to be sister-group to an haplogroup restricted to West Papua and the Coral Sea, yielding evidence of recent secondary westward colonization. Such a complex structure is in sharp contrast with the generally weak phylogeographic patterns uncovered to date in other widely distributed, large pelagic fishes with pelagic eggs and larvae. We hypothesize that in S. commerson and possibly other Scomberomorus species, philopatric migration may play a role in maintaining the geographic isolation of populations by annihilating the potential consequences of passive dispersal.
Biological Journal of the Linnean Society

ird-00759711
http://hal.ird.fr/ird-00759711
http://hal.ird.fr/ird-00759711/document

Éditeur(s) : HAL CCSD Linnean Society of London
Résumé : International audience
Although migratory pelagic fishes generally exhibit little geographic differentiation across oceans, as expected from their life-history (broadcast spawning, pelagic larval life, swimming ability of adults) and the assumed homogeneity of the pelagic habitat, exceptions to the rule deserve scrutiny. One such exception is the narrow-barred Spanish mackerel (Scomberomorus commerson), where strong genetic heterogeneity at the regional scale has been previously reported. We investigated the genetic composition of S. commerson across the Indo-West Pacific range using control-region sequences (including previously published datasets), cytochrome-b gene partial sequences, and eight microsatellite loci, to further explore its phylogeographic structure. All haplotypes sampled from the Indo-Malay-Papua archipelago (IMPA) and the southwestern Pacific coalesced into a clade (Clade II) that was deeply separated (14.5% nucleotide divergence) from a clade grouping all haplotypes from the Persian Gulf and Oman Sea (Clade I). Such a high level of genetic divergence suggested the occurrence of two sister-species. Further phylogeographic partition was evident between the western IMPA and the regions sampled east and south of it, i.e. northern Australia, West Papua, and the Coral Sea. Strong allele-frequency differences were found between local populations in the southwestern Pacific, both at the mitochondrial locus (ΦST=0.282-0.609) and at microsatellite loci (^θ=0.202-0.313). Clade II consisted of four deeply divergent subclades (9.0-11.8% nucleotide divergence for the control region; 0.3-2.5% divergence at the cytochrome b locus). Mitochondrial sub-clades within Clade II generally had narrow geographic distribution, demonstrating further genetic isolation. However, one particular haplogroup within Clade II was present throughout the central Indo-West Pacific; that haplogroup was found to be sister-group to an haplogroup restricted to West Papua and the Coral Sea, yielding evidence of recent secondary westward colonization. Such a complex structure is in sharp contrast with the generally weak phylogeographic patterns uncovered to date in other widely distributed, large pelagic fishes with pelagic eggs and larvae. We hypothesize that in S. commerson and possibly other Scomberomorus species, philopatric migration may play a role in maintaining the geographic isolation of populations by annihilating the potential consequences of passive dispersal.
ISSN: 0024-4066

ird-00759711
http://hal.ird.fr/ird-00759711
http://hal.ird.fr/ird-00759711v2/document
http://hal.ird.fr/ird-00759711/file/FauvelotBorsa_Scomberomorus%20commerson%20p%20HAL.pdf

Éditeur(s) : HAL CCSD Wiley
Résumé : [b]Aim[/b][br/] Many tropical tree species have poorly delimited taxonomic boundaries and contain undescribed or cryptic species. We examined the genetic structure of a species complex in the tree genus Carapa in the Neotropics in order to evaluate age, geographic patterns of diversity and evolutionary relationships, and to quantify levels of introgression among currently recognized species.[br/] [br/] [b]Location[/b][br/] Lowland moist forests in the Guiana Shield, the Central and Western Amazon Basin, Chocó and Central America.[br/] [br/] [b]Methods[/b][br/] Genetic structure was analysed using seven nuclear simple sequence repeats (nuSSR), five chloroplast SSRs (cpSSR), and two chloroplast DNA (cpDNA) intergenic sequences (trnH-psbA and trnC-ycf6). Bayesian clustering analysis of the SSR data was used to infer population genetic structure and to assign 324 samples to their most likely genetic cluster. Bayesian coalescence analyses were performed on the two cpDNA markers to estimate evolutionary relationships and divergence times.[br/] [br/] [b]Results[/b][br/] Two genetic clusters (nu_guianensis and nu_surinamensis) were detected, which correspond to the Neotropical species C. guianensis (sensu latu) and C. surinamensis. Fourteen cpDNA haplotypes clustered into six haplogroups distributed between the two nuclear genetic clusters. Divergence between the haplogroups was initiated in the Miocene, with some haplotype structure evolving as recently as the Pleistocene. The absence of complete lineage sorting between the nuclear and chloroplast genomes and the presence of hybrid individuals suggest that interspecific reproductive barriers are incomplete. NuSSR diversity was highest in C. guianensis and, within C. guianensis, cpDNA diversity was highest in the Central and Western Amazon Basin. Regional genetic differentiation was strong but did not conform to an isolation-by-distance process or exhibit a phylogeographical signal.[br/] [br/] [b]Main conclusions[/b][br/] The biogeographical history of Neotropical Carapa appears to have been influenced by events that took place during the Neogene. Our results point to an Amazonian centre of origin and diversification of Neotropical Carapa, with subsequent migration to the Pacific coast of South America and Central America. Gene flow apparently occurs among species, and introgression events are supported by inconsistencies between chloroplast and nuclear lineage sorting. The absence of phylogeographical structure may be a result of the ineffectiveness of geographical barriers among populations and of reproductive isolation mechanisms among incipient and cryptic species in this species complex.
ISSN: 0305-0270

hal-01032395
https://hal.archives-ouvertes.fr/hal-01032395
DOI : 10.1111/j.1365-2699.2011.02678.x

Éditeur(s) : Wiley-blackwell
Résumé : The reef fauna connectivity of the West Indian Ocean (WIO) is one of the least studied globally. Here we use genetic analyses of the grouper Epinephelus merra (Bloch 1793) to determine patterns of connectivity and to identify barriers to dispersal in this WIO marine area. Phylogeographic and population-level analyses were conducted on cytochrome b sequences and microsatellites (13 loci) from 557 individuals sampled in 15 localities distributed across the West Indian Ocean. Additional samples from the Pacific Ocean were used to benchmark the WIO population structure. The high level of divergence revealed between Indian and Pacific localities (of about 4.5% in sequences) might be the signature of the major tectonic and climatic changes operating at the Plio-Pleistocene transition, congruently with numerous examples of Indo-Pacific speciation. In comparison, the E. merra sequences from the Indian Ocean constitute a monophyletic clade with a low average genetic distance (d < 0.5%). However both genetic markers indicated some structure within this ocean. The main structure revealed was the isolation of the Maldives from the WIO localities (a different group signature identified by clustering analysis, great values of differentiation). Both marker types reveal further significant structure within the WIO, mainly the isolation of the Mascarene Islands (significant AMOVA and isolation-by-distance patterns) and some patchy structure between the northernmost localities and within the Mozambique Channel. The WIO genetic structure of E. merra appeared congruent with main biogeographic boundaries and oceanographic currents.
Marine Ecology-an Evolutionary Perspective (0173-9565) (Wiley-blackwell), 2015-09 , Vol. 36 , N. 3 , P. 447-461

Droits : 2014 Blackwell Verlag GmbH
http://archimer.ifremer.fr/doc/00189/30046/28566.pdf
DOI:10.1111/maec.12153
http://archimer.ifremer.fr/doc/00189/30046/

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
AimThe global biodiversity crisis requires the identification of regions with high evolutionary potential, i.e. evolutionary hotspots (evospots). We created an analytical framework based on comparative phylogeography and coalescent methods to assess the dynamics of diversification and population persistence in the reef ecosystem of a little-studied region: the Southwestern Indian Ocean (SWIO).LocationCoral reefs of the SWIO, with comparative data from the Pacific Ocean.MethodsWe generated sequences of mitochondrial DNA (COI and 16S) for 10 widespread brittle-stars (345 specimens) from 21 localities (8 in the SWIO). We analysed them by combining comparative phylogeography approaches, coalescent-based methods, molecular clocks and the concept of evolutionarily significant units (ESUs) to draw conclusions about the drivers of biodiversity in the region.ResultsCryptic diversity was prevalent, increasing lineage diversity within the 10 nominal species by 70% within the SWIO and by 200% across the Indo-West Pacific. All seven new SWIO lineages meet the criteria for ESUs and at least six are biological species. We detected likely intraregional diversifications dating to the Plio-Pleistocene, supporting the SWIO as a generator of biodiversity. Geographical restriction of ESUs, long coalescent times (> 80 ka) and old in situ diversification (> 1 Ma) point to the persistence of populations over multiple glacio-eustatic cycles. We provide data suggesting demographic expansion during sea-level high stands. Regional connectivity was lower, and cryptic differentiation higher in lecithotrophs than in planktotrophs.Main conclusionsThe analytical framework based on a biodiversity survey makes it possible to identify evospots by assessing the potential of a region to maintain and generate biodiversity and by evaluating the evolutionary processes and potential drivers at play.
ISSN: 0305-0270

hal-01369697
http://hal.univ-reunion.fr/hal-01369697
DOI : 10.1111/jbi.12155

Éditeur(s) : World Aquaculture Society
Résumé : Mangrove oysters encompass several species and their taxomony is unclear. Among then, Crassostrea rhizophorae has been described along the Central and South American Atlantic coasts and Crassostrea gasar along African Atlantic coasts. Most taxonomic studies have so far been based on morphological criteria which are particularly susceptible to plasticity and new insight can be provided by molecular markers. The present work aims to provide information on the phylogeography of these two taxa.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2000/acte-3496.pdf
http://archimer.ifremer.fr/doc/00000/3496/

Éditeur(s) : HAL CCSD Thai Society of Higher Education Institutes on Environment
Résumé : International audience
Due to the high level of endemic species that they support and the high threats they are facing, such as unsustainable limestone quarrying, hunting and urbanization, limestone karsts are recognized as biodiversity hotspots needing urgent protection. The first aim of our study was to investigate the mammal rodent diversity of Thai limestone karsts. Our second aim was to examine the diversity at a finer scale than the species level (intraspecific biodiversity) using phylogeographic approaches. Therefore, we studied the phylogeographic structure of a threatened rodent, endemic to limestone karsts of Thailand, the Murinae Leopoldamys neilli. We sampled 76 limestone karsts in whole Thailand and live-trapped 444 rodents including 115 Leopoldamys neilli. Our study revealed an important rodent diversity in Thai limestone karsts. Besides endemic rodent species, karsts also host typical forest species to which they provide forest refugia in deforested regions. At the intraspecific level, our study revealed an unexpected high level of genetic differentiation within the rodent species L. neilli. As each limestone area of Thailand is characterized by a particular genetic lineage of L. neilli, the destruction of these karsts would lead to the disappearance of unique intraspecific strains not found elsewhere. Our results highlight the importance of protecting limestone habitats to preserve not only their interspecific but also intraspecific rodent diversity that is highly threatened as more than 20% of limestone karsts in Thailand have already been quarried. Management plans of limestone, a non-renewable resource, should urgently take into account this high biological importance of karsts.
The 1st EnvironmentAsia International Conference on "Environmental Supporting in Food and Energy Security: Crisis and Opportunity"
Bangkok, Thailand

ird-00714455
http://hal.ird.fr/ird-00714455
http://hal.ird.fr/ird-00714455/document
IRD : fdi:010056152

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : Simple sequence repeat (SSR) markers are widely used tools for inferences about genetic diversity, phylogeography and spatial genetic structure. Their applications assume that variation among alleles is essentially caused by an expansion or contraction of the number of repeats and that, accessorily, mutations in the target sequences follow the stepwise mutation model (SMM). Generally speaking, PCR amplicon sizes are used as direct indicators of the number of SSR repeats composing an allele with the data analysis either ignoring the extent of allele size differences or assuming that there is a direct correlation between differences in amplicon size and evolutionary distance. However, without precisely knowing the kind and distribution of polymorphism within an allele (SSR and the associated flanking region (FR) sequences), it is hard to say what kind of evolutionary message is conveyed by such a synthetic descriptor of polymorphism as DNA amplicon size. In this study, we sequenced several SSR alleles in multiple populations of three divergent tree genera and disentangled the types of polymorphisms contained in each portion of the DNA amplicon containing an SSR. The patterns of diversity provided by amplicon size variation, SSR variation itself, insertions/deletions (indels), and single nucleotide polymorphisms (SNPs) observed in the FRs were compared. Amplicon size variation largely reflected SSR repeat number. The amount of variation was as large in FRs as in the SSR itself. The former contributed significantly to the phylogenetic information and sometimes was the main source of differentiation among individuals and populations contained by FR and SSR regions of SSR markers. The presence of mutations occurring at different rates within a marker's sequence offers the opportunity to analyse evolutionary events occurring on various timescales, but at the same time calls for caution in the interpretation of SSR marker data when the distribution of within-locus polymorphism is not known.
ISSN: 1932-6203

hal-01190764
https://hal.archives-ouvertes.fr/hal-01190764
PRODINRA : 214530
PUBMED : 22808236
DOI : 10.1371/journal.pone.0040699

Éditeur(s) : HAL CCSD Wiley
Résumé : [b]Aim[/b][br/] [br/] The phylogeographical history of Neotropical species can be difficult to reconstruct because of superimposed Neogene and Quaternary histories, and because of taxonomic uncertainty. We analysed range-wide genetic diversity in a widespread pioneer tree species, Jacaranda copaia (Aubl.) D. Don, to characterize phylogeographical structure, date the evolutionary relationships among lineages, and evaluate the role of dispersal and vicariance in establishing the present geographical range.[br/] [br/] [br/] [b]Location[/b][br/] [br/] Guiana Shield; central, southern and western Amazon Basin; Chocó region; Central America.[br/] [br/] [br/] [b]Methods[/b][br/] [br/] We analysed nine nuclear simple sequence repeat loci (nuSSR), eight chloroplast SSRs (cpSSR), and two cpDNA intergenic sequences in 341 adult trees. Genetic differentiation at nuSSRs was inferred using Bayesian clustering. Dating of chloroplast lineage divergence was obtained using a range of published mutation rates and Bayesian coalescence analyses. Population divergence dating was performed using an isolation-with-migration model for eight loci (one cp sequence and seven nuSSRs).[br/] [br/] [br/] [b]Results[/b][br/] [br/] Nuclear SSR variation identified three geographically overlapping clusters (nu-1, nu-2, nu-3). Twelve cpDNA haplotypes were clustered into two haplogroups (cp-1, cp-2) with the central Amazon harbouring the highest diversity. Molecular dating analysis suggests that cpDNA haplotype diversification started around the end of the Pliocene (2.61 Ma on average), whereas population divergence was more recent and occurred during the mid-Quaternary (point estimates between 357 and 436 ka).[br/] [br/] [br/] [b]Main conclusions[/b][br/] [br/] The genetic variation of J. copaia in the Neotropics was shaped mainly by Pleistocene events. Chloroplast diversity did not display the expected cis/trans Andean disjunction, indicating recent dispersal. Nuclear variation revealed that separate regions share a recent history, with a centre of diversity in the central Amazon Basin. The geographical pattern of diversity is congruent with the distribution of the two subspecies, J. copaia copaia and J. copaia spectabilis, and evidence of nuSSR admixture between the two taxa supports their classification as subspecies.
ISSN: 0305-0270

hal-01032410
https://hal.archives-ouvertes.fr/hal-01032410
DOI : 10.1111/j.1365-2699.2012.02797.x

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
The Black Rat (Rattus rattus) spread out of Asia to become one of the world's worst agricultural and urban pests, and a reservoir or vector of numerous zoonotic diseases, including the devastating plague. Despite the global scale and inestimable cost of their impacts on both human livelihoods and natural ecosystems, little is known of the global genetic diversity of Black Rats, the timing and directions of their historical dispersals, and the risks associated with contemporary movements. We surveyed mitochondrial DNA of Black Rats collected across their global range as a first step towards obtaining an historical genetic perspective on this socioeconomically important group of rodents. We found a strong phylogeographic pattern with well-differentiated lineages of Black Rats native to South Asia, the Himalayan region, southern Indochina, and northern Indochina to East Asia, and a diversification that probably commenced in the early Middle Pleistocene. We also identified two other currently recognised species of Rattus as potential derivatives of a paraphyletic R.rattus. Three of the four phylogenetic lineage units within R. rattus show clear genetic signatures of major population expansion in prehistoric times, and the distribution of particular haplogroups mirrors archaeologically and historically documented patterns of human dispersal and trade. Commensalism clearly arose multiple times in R. Rattus and in widely separated geographic regions, and this may account for apparent regionalism in their associated pathogens. Our findings represent an important step towards deeper understanding the complex and influential relationship that has developed between Black Rats and humans, and invite a thorough re-examination of host-pathogen associations among Black Rats.
PLoS ONE

ird-00714383
http://hal.ird.fr/ird-00714383
http://hal.ird.fr/ird-00714383/document
DOI : 10.1371/journal.pone.0026357
IRD : fdi:010055548

Éditeur(s) : HAL CCSD Cambridge University Press
Résumé : International audience
Genetic variation was examined in two complex cases of Indo-Pacific pygmy angelfishes (genus Centropyge; Pomacanthidae). The lemonpeel pygmy angelfish C. flavissima (Cuvier and Valenciennes) has a geographically disjunct Indian vs. Pacific distribution and the individuals from these two regions differ by their colour patterns. Previous research on C. flavissima has shown mitochondrial introgression from two related species, C. eibli in the eastern Indian Ocean and C. vrolikii in the Pacific Ocean. Using the 16S rDNA and the CO1 gene as phylogeographic markers, we found no mitochondrial haplotypes in common between Indian Ocean C. flavissima and C. eibli, confirming partial genetic isolation, albeit recent. Also, we found substantial genetic differences between Indian and Pacific C. flavissima populations at the nuclear ETS-2 intron locus. The Indian Ocean form of C. flavissima, thus geographically isolated by >2000 km distance from its Pacific Ocean counterpart, is described as a new species, Centropyge cocosensis sp. nov. Centropyge cocosensis sp. nov. differs in appearance from C. flavissima in having a conspicuous blue iris and a fainter, bluish eye ring. We also found that the yellow pygmy angelfish C. heraldi Woods and Schultz consists of two genetically distinct entities, one distributed widely in the northern tropical Indo-West Pacific, the other distributed in the southern Pacific Ocean. The name originally given to the blackfin pygmy angelfish, C. woodheadi Kuiter, is here resurrected to designate the latter.
EISSN: 1755-2672

hal-01340521
https://hal-univ-perp.archives-ouvertes.fr/hal-01340521
DOI : 10.1007/s12526-016-0509-y

Éditeur(s) : HAL CCSD Frontiers Media
Résumé : The disease, Heartwater, caused by the Anaplasmataceae E. ruminantium, represents a major problem for tropical livestock and wild ruminants. Up to now, no effective vaccine has been available due to a limited cross protection of vaccinal strains on field strains and a high genetic diversity of Ehrlichia ruminantium within geographical locations. To address this issue, we inferred the genetic diversity and population structure of 194 E. ruminantium isolates circulating worldwide using Multilocus Sequence Typing based on lipA, lipB, secY, sodB, and sucA genes. Phylogenetic trees and networks were generated using BEAST and SplitsTree, respectively, and recombination between the different genetic groups was tested using the PHI test for recombination. Our study reveals the repeated occurrence of recombination between E. ruminantium strains, suggesting that it may occur frequently in the genome and has likely played an important role in the maintenance of genetic diversity and the evolution of E. ruminantium. Despite the unclear phylogeny and phylogeography, E. ruminantium isolates are clustered into two main groups: Group 1 (West Africa) and a Group 2 (worldwide) which is represented by West, East, and Southern Africa, Indian Ocean, and Caribbean strains. Some sequence types are common between West Africa and Caribbean and between Southern Africa and Indian Ocean strains. These common sequence types highlight two main introduction events due to the movement of cattle: from West Africa to Caribbean and from Southern Africa to the Indian Ocean islands. Due to the long branch lengths between Group 1 and Group 2, and the propensity for recombination between these groups, it seems that the West African clusters of Subgroup 2 arrived there more recently than the original divergence of the two groups, possibly with the original waves of domesticated ruminants that spread across the African continent several thousand years ago.
ISSN: 2235-2988

hal-01594501
https://hal.archives-ouvertes.fr/hal-01594501
https://hal.archives-ouvertes.fr/hal-01594501/document
https://hal.archives-ouvertes.fr/hal-01594501/file/paper_MLST_ER_2016_%7B51027B58-C2C7-41C8-9746-BD8A9F387C87%7D.pdf
DOI : 10.3389/fcimb.2016.00111

Éditeur(s) : Blackwell science
Résumé : Patterns of mitochondrial DNA (mtDNA) variation were used to analyse the population genetic structure of southwestern Indian Ocean green turtle (Chelonia mydas) populations. Analysis of sequence variation over 396 bp of the mtDNA control region revealed seven haplotypes among 288 individuals from 10 nesting sites in the Southwest Indian Ocean. This is the first time that Atlantic Ocean haplotypes have been recorded among any Indo-Pacific nesting populations. Previous studies indicated that the Cape of Good Hope was a major biogeographical barrier between the Atlantic and Indian Oceans because evidence for gene flow in the last 1.5 million years has yet to emerge. This study, by sampling localities adjacent to this barrier, demonstrates that recent gene flow has occurred from the Atlantic Ocean into the Indian Ocean via the Cape of Good Hope. We also found compelling genetic evidence that green turtles nesting at the rookeries of the South Mozambique Channel (SMC) and those nesting in the North Mozambique Channel (NMC) belong to separate genetic stocks. Furthermore, the SMC could be subdivided in two different genetic stocks, one in Europa and the other one in Juan de Nova. We suggest that this particular genetic pattern along the Mozambique Channel is attributable to a recent colonization from the Atlantic Ocean and is maintained by oceanic conditions in the northern and southern Mozambique Channel that influence early stages in the green turtle life cycle.
Molecular Ecology (0962-1083) (Blackwell science), 2007 , Vol. 16 , N. 1 , P. 175-186

Droits : 2007 Blackwell
http://archimer.ifremer.fr/doc/2007/publication-2185.pdf
DOI:10.1111/j.1365-294X.2006.03122.x
http://archimer.ifremer.fr/doc/00000/2185/

Éditeur(s) : World Aquaculture Society, Aquaculture 2006
Résumé : Oysters are among the most familiar of all marine invertebrate taxa. However our knowledge of oyster phylogeny and systematics is fragmentary. This is principally due to the plastic growth patterns of these animals, which result in a wide range of overlapping, ecophenotypic variants that greatly reduce the value of analysis based on shell morphology. Besides that, many intentional or accidental anthropogenic transfers have emphasised this situation. In several cases of misclassification or misidentification of oysters, DNA molecular data, have provided valuable new insights on the tracing of introductions or more generally on the phylogeographic relationships between oyster species. We will illustrate this issue with recent case studies from our lab on several flat and cupped oysters: (1) the Crassostrea gigas – Crassostrea angulata couple of Asian species and their successive introductions in Europe, (2) the new species of cupped oysters, Crassostrea honkongensis, described in Hong-Kong and very divergent from the species Crassostrea gigas it was initially supposed to be, (3) the mangrove oyster Crassostrea gasar that was shown not only to be present along the coasts of Western Africa but also along the Atlantic coasts of South America, and (4) the geographic disjunction between Ostreola stentina, described in the Mediterranean Sea, and the genetically closely related species Ostrea aupouria (from New Zealand) and Ostreola equestris (from Mexico Gulf/Atlantic). At the intra specific level, we will focus on one of the main documented case in Europe, the flat oyster, Ostrea edulis. It is a marine bivalve whose natural geographical distribution ranges along the European Atlantic coast from Norway to Morocco, in addition to the Mediterranean and Black Sea. Studies of allozymes, microsatellites and mitochondrial differentiation over the whole range concluded that a significant divergence existed between Mediterranean and Atlantic populations, together with an isolation-by-distance pattern. However, the average mitochondrial haplotypic diversity displayed a high among populations variance, reflecting smaller effective population size in some locations. Additionally, a ten-fold quantitative difference was observed in the same study in Fst between the mitochondrial and the nuclear genomes, which could be due to sex biased differential reproductive success between males and females. In order to further document this hypothesis, two experiments at the population level were conducted. First, brooding females were sampled in a wild population and the number of males fertilizing a given female estimated. Then, parentage analyses were achieved under experimental conditions: successive mass spawnings were collected from a population of potential genitors kept in hatchery, whose genotypes were known, in order to infer a posteriori the relative contribution of each genitor. Moreover, we aimed to better understand the reproduction dynamics of this species. Several patterns of spawning could be distinguished: unique, successive or extended in time. The different parental contributions and reproductive behaviors observed in these experiments are discussed in the context of the hypothesis of a variance in the reproductive success of males and females and consequences in local and temporal reduced effective population sizes.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2006/acte-3475.pdf
http://archimer.ifremer.fr/doc/00000/3475/

Résumé : Three species of man.-rove oysters, Crassostrea rhizophorae, C. brasiliana, and C. gasar, have been described along the Atlantic shores of South America and Africa. Because the distribution of these molluscs is of great biological and commercial interest, their taxonomy and distribution deserve further clarification. Therefore, 15 populations were sampled from both continents. Their 16S mitochondrial polymorphism was studied by sequencing and PCR-RFLP analysis. Two haplotypes were identified. Haplotype a was the only one observed in Africa, but it was also observed in South America together with haplotype b. Because C. gasar is the only mangrove oyster identified on the west coast of Africa, haplotype a was attributed to this species, which has thus been shown to occur in South America. Haplotype b is attributed to C. rhizophorae. The karyotypes of specimens of C. gasar, from Africa and from South America, were very similar, and both species were observed at the same location in Brazil. The occurrence of C. gasar in South America adds a third species-in addition to C rhizophorae and C. brasiliana-to the list of species present along these coasts. The predominant surface circulation patterns in this part of the Atlantic Ocean favor the hypothesis that C. gasar was transported from Africa to America. Finally, a phylogenetic tree built with seven 16S sequences from Crassostrea and Saccostrea species showed that C. gasar is intermediate between the American Crassostrea species (C virginica and C. rhizophorae) and the Asian species (C. gigas and C ariakensis).
Biological Bulletin (0006-3185), 2002-06 , Vol. 202 , N. 3 , P. 232-242

Droits : Marine Biological Laboratory.
http://archimer.ifremer.fr/doc/2002/publication-2790.pdf
http://archimer.ifremer.fr/doc/00000/2790/

Résumé : La tuberculose, maladie très ancienne, est plus que jamais présentée sur la scène sanitaire mondiale avec 9 millions de nouveaux cas par an. Cette maladie, qui demeure une cause majeure de mortalité, est un des problèmes les plus difficiles à résoudre en santé publique et à échelle internationale. Les diverses programmes de lutte, lancés par l’Organisation Mondiale de la Santé (OMS), pour prévenir et garantir la guérison des patients tuberculeux, se heurtent à des difficultés qui hypothèquent leur efficacité. En effet, l'expansion du virus de rinimunodéficience humaine (VIII) et son influence néfaste sur la susceptibilité à la tuberculose, l'accroissement rapide de la tuberculose multirésistante, la pauvreté ainsi que la croissance démographique, sont un ensemble de facteurs préjudiciables à l'application des mesures préventives et curatives. Les contextes économiques difficiles conduisant indubitablement au cumul de ces facteurs, ont fait une césure entre les pays riches et les pays pauvres quant à l'incidence et la révolution de la tuberculose à échelle mondiale. Pour atténuer la disparité des résultats des luttes antituberculeuses, les méthodologies employées en épidémiologie de la tuberculose doivent s'inscrire dans une démarche d'efficacité. Les marqueurs moléculaires, indispensables à l'identification et à la classification des souches appartenant au complexe Mycobacterium tuberculosis (MTC) ont chacun des potentialités qui leur sont propres dont il convient de cerner pour une utilisation adéquate dans les études épidémiologiques et phylogénétiques. Le but de cette thèse consiste à extraire des connaissances nouvelles des résultats de génotypage stockées dans les bases de données, connaissances relatives au polymorphisme du support génomique pour estimer la contribution de chaque marqueur dans la classification de MTC. Le recours à différentes méthodes de reconstruction phylogénétique et de modélisation des données fut indispensable. A la lumière des résultats obtenus, cette thèse propose une nouvelle méthodologie de classification, pour rétablissement d'une phylogéographie robuste de MTC en relation avec l'histoire des migrations humaines qui aurait débutée en Afrique subsaharienne. Chaque méthode de génotypage ayant une efficience et un cout propres, qu'il convient de mesurer par rapport aux moyens disponibles et aux résultats escomptes, il est donc intéressant de renforcer la connaissance des marqueurs et de proposer différentes alternatives menant à la classification des mycobactéries. Ainsi, les résultats obtenus dans cette thèse apportent plus de cohérence aux solutions proposées pour la caractérisation des clones de MTC circulant dans le monde.
Tuberculosis, very old disease, is more than ever presented on the global health scene with 9 million new cases per year. This disease, which remains a major cause of mortality is one of the most intractable public health and international issues. The various control programs, launched by the World Health Organization (WHO) to prevent and guarantee the cure of tuberculosis patients face difficulties that undermine their effectiveness. Indeed, the expansion of human virus rinimunodéficience (VIII) and its negative influence on susceptibility to tuberculosis, the rapid growth of multidrug-resistant tuberculosis, poverty and population growth, are a set of factors detrimental to application of preventive and curative measures. The difficult economic circumstances undoubtedly leading to accumulation of these factors have a break between rich and poor countries about the impact and the revolution of tuberculosis worldwide. To address the disparity of the results of tuberculosis struggles, the methodologies used in epidemiology of tuberculosis must be part of a process efficiency. Molecular indispensable to the identification and classification of strains belonging to the Mycobacterium tuberculosis complex (MTC) markers each have their own potentials that need to be identified for proper use in epidemiological and phylogenetic studies. The purpose of this thesis is to extract new knowledge of the results of genotyping data stored in databases, knowledge of the polymorphism of genomic carrier to estimate the contribution of each marker in the classification of TCM. The use of different methods of phylogenetic reconstruction and modeling data was essential. In light of the results obtained, the thesis proposes a new classification methodology for a robust recovery phylogeography of TCM in connection with the history of human migration have started in sub-Saharan Africa. Each genotyping method with cost efficiency and equity, should be measured in relation to the resources available and discounts results, it is interesting to strengthen the knowledge of markers and propose alternatives leading to the classification of mycobacteria. Thus, the results obtained in this thesis bring more coherence to the proposed characterization of clones MTC circulating worldwide solutions.

http://www.theses.fr/2012AGUY0518/document

Résumé : La distribution actuelle des espèces d’arbres des forêts tropicales humides amazoniennes est le résultat de processus dynamiques sur lesquels les perturbations passées, d’origine climatique ou anthropique, peuvent avoir jouées un rôle majeur. Des outils génétiques actuels associés à des méthodes d’analyses puissantes permettent d’inférer et de dater l’empreinte génomique des évènements démographiques subits par les populations naturelles. Le but de cette thèse est de contribuer à une vision d’ensemble de l’évolution démographique de la forêt tropicale humide du plateau des Guyanes pendant le Quaternaire. J’ai d’abord étudié les propriétés des microsatellites (répétitions simple de séquences, SSR) et les limites de leurs applications en tant que marqueurs moléculaires en phylogéographie. Plusieurs allèles SSR contenu dans diverses populations de trois genres d’arbres différents ont été séquencés et le polymorphisme, porté par chaque partie des fragments ADN contenant des SSR, a été étudié. J’ai observé que la quantité de variation génétique était aussi importante dans les régions encadrant le microsatellite que dans le SSR lui-même. Ces régions ont contribué significativement à l’information phylogénétique et ont parfois été la principale source de différenciation entre les individus et les populations. Cette expérience m’a permis de choisir la meilleure stratégie à adopter pour traiter les données de variation génétique des SSR dans des modèles démographiques. J’ai ensuite utilisé ces marqueurs SSR et des méthodes ABC pour étudier l’impact local des occupations humaines précolombiennes sur les forêts en Guyane française. Les changements démographiques subis par des populations de quatre espèces d’arbres ont été comparés entre cinq sites occupés et quatre sites non perturbés. Les perturbations naturelles et induites par l’homme ont contribué à la mise en place de la diversité observée actuellement, comme le suggère des signatures d’effet fondateur détectées sur les sites perturbés ou non. Néanmoins, la taille des populations fondatrices semble être proportionnelle à l’impact humain estimé, indiquant que les perturbations anthropique ont induit un remplacement des populations plus important que les processus écologiques naturels. Pour terminer, j’ai mené une étude de démographie comparative d’espèces d’arbres tropicaux à l’échelle régionale de la Guyane française. Cinq scénarios démographiques ont été testés pour neuf populations de huit espèces en utilisant des microsatellites nucléaires et des séquences chloroplastiques. Les changements démographiques les plus récents détectés convergent vers une signature générale d’expansion de la forêt humide depuis probablement la dernière glaciation. Cela peut suggérer, soit que la composition des forêts du plateau des Guyanes était différente, ou que le couvert forestier était moins étendu. Ce résultat constitue le premier indice de changement passé, probablement d’origine climatique, subi par les communautés forestières du plateau des Guyanes ; qui n’avait jusque-là pas pu être testé avec des méthodes standards en raison d’un manque de fossiles. En conclusion, j’ai recueilli des preuves génétiques que les perturbations, à différents échelles de temps, ont marqué la structure et la composition génétique des forêts du plateau des Guyanes. L’application de ces méthodes à d’autres régions Néotropicales pourrait contribuer, à l’avenir, à reconstruire l’histoire écologique de la forêt amazonienne de façon détaillée.
The current tree species distribution in Amazonian tropical rainforests is the outcome of dynamic processes in which past perturbations, climatic or anthropogenic, may have played a major role. Currently available genetic tools associated with powerful analytical methods allow inferring and dating the genomic imprint of demographic events undergone by natural populations. The aim of my thesis is to contribute to an overview of the demographic evolution of the tropical rainforest in the Guiana shield during the Quaternary. I have first studied the properties of microsatellites or Simple sequence repeat (SSR) and the limits in their applications as molecular markers in phylogeography. Several SSR alleles in multiple populations of three divergent tree genera have been sequenced and the sources of polymorphisms, carried by each portion of SSR-containing DNA amplicons, have been broken apart. I have observed that the amount of variation was as large in flanking regions as in the SSR itself. The former contributed significantly to the phylogenetic information and sometimes was the main source of differentiation among individuals and populations. This experiment allowed me to choose the best strategy to treat SSR variation in demographic modeling. I have subsequently used SSR markers and ABC methods to study the impact of pre-Columbian human settlements at the local level on rainforests in French Guiana. Demographic changes undergone by populations of four tree species were compared between five settled and four undisturbed sites. Both natural turnover and human-induced disturbances appeared as shaping currently observed genetic diversity, with signatures of founder effect both at disturbed and undisturbed sites. Nevertheless, the size of founding populations appeared to be proportional to the estimated human impact, suggesting that human-made disturbance caused deeper population turnover than background ecological processes. Finally, I have conducted a comparative demography study of tropical tree species at the regional level across French Guiana. Five demographic scenarios have been tested for nine populations from eight species using both nuclear microsatellites and chloroplastic sequences. The most recent demographic signals detected converge on a global signature of expansion of the rainforest since probably the last glaciation. This finding can suggest either that the composition of the Guiana shield rainforests was different, or that its global extent was smaller, during earlier epochs of the Pleistocene than today. This result is the first firm indication of changes undergone by the forest communities of the Guiana shield in the distant climatic past – something which could not be tested with standard methods due to almost complete lack of fossil evidence. In conclusion, I have gathered genetic evidence that disturbances, both in historical and geological times, have marked the structure and composition of forests in the Guiana shield.The extensive application of these methods to other regions of the Neotropics maycontribute, in the future, to the detailed reconstruction of the ecological history ofAmazonian forests.

http://www.theses.fr/2012AGUY0568/document

Résumé : La tuberculose (TB), maladie infectieuse contagieuse, est causée par une mycobactérie appartenant au complexe Mycobacterium tuberculosis (MTBC). Malgré de nombreuses campagnes de vaccination par le BCG (Bacilles de Calmette et Guérin) et les traitements antituberculeux, on observe une réémergence de la maladie depuis les années 80. Ce bouleversement s’explique par la coïnfection avec le virus du VIH/SIDA, la désorganisation des systèmes de santé et par l’apparition des bactéries résistantes aux principaux antibiotiques antituberculeux. Dans ce contexte une meilleure connaissance des mouvements et de l’évolution des clones circulants du bacille tuberculeux permettrait de détecter plus rapidement et de façon plus pertinente l’émergence d’épidémies. Le contrôle et la surveillance de la maladie représentent des moyens essentiels pour lutter contre l’expansion mondiale de la tuberculose. C’est ainsi que l’unité de la Tuberculose et des Mycobactéries de l’Institut Pasteur de la Guadeloupe (IPG) a mis en place une base de données de profils génotypiques pour l’étude de l’épidémiologie globale de la tuberculose. Dans le cadre de cette thèse, nous décrirons les méthodes de bioinformatique qui ont été utilisées pour la gestion et l’exploitation de la 6ème version (SITVIT2) de cette base de données des génotypes pour mieux comprendre l’évolution et la dissémination mondiale du bacille tuberculeux. Cette base intègre aussi plusieurs marqueurs moléculaires tels que les MIRU-VNTRs (« mycobacterial interspersed repetitive units-variable number of tandem repeats ») et le Spoligotype43 servant à mieux décrire et identifier les familles de profils génotypiques du MTBC. La banque de données SITVIT2 ne cesse d’évoluer, et elle contient actuellement des informations épidémiologiques sur 111 635 isolats cliniques. Cette base de données est consultable en ligne à l’adresse suivante : http://www.pasteur-guadeloupe.fr:8081/SITVIT2/. Nous avons également réalisé une base de données nommée SITVITBovis qui est dédiée à la tuberculose bovine. Cette base de données sera accessible à l’adresse : http://www.pasteur-guadeloupe.fr:8081/SITVIT_Bovis/. Parallèlement au développement et à la gestion des bases de données, ce travail de thèse s’est appuyé sur plusieurs études épidémiologiques et phylogéographiques mettant en corrélation les données disponibles sur la résistance aux médicaments ou les caractéristiques démographiques (dont le sexe, l’âge, le statut VIH, et l’origine du patient). Notre initiative de recherche permet ainsi d’améliorer la caractérisation phylogénétique détaillée des lignées du MTBC, ainsi que l’épidémiologie des clones en circulation, afin d’élaborer une cartographie géographique des isolats cliniques prédominants pour les bacilles tuberculeux principalement impliqués dans la maladie, à l’échelle nationale, régionale et mondiale. La superposition ultérieure de ces cartes avec des données sociopolitiques, économiques et démographiques obtenues auprès de Systèmes d’information géographique (SIG) ont permis de dresser un portrait précis des disparités actuelles par pays ou sous-région. Cette thèse représente une importante collaboration avec plusieurs équipes de chercheurs travaillant également dans le domaine de l’épidémiologie moléculaire de la tuberculose. L’objectif à long terme de ce travail, est d’optimiser la structure de la base, et de pérenniser l’enrichissement de celle-ci (notamment par l’automatisation et la facilité de la saisie de données). Une représentation optimale et une meilleure accessibilité des données de la base conforteraient les efforts faits pour le contrôle et la surveillance de la TB dans monde.
Tuberculosis (TB) is a contagious infectious disease caused by mycobacteria belonging to the Mycobacterium tuberculosis complex (MTBC). Despite numerous campaigns of vaccination by the BCG (Bacillus Calmette-Guérin) vaccine, and TB treatments, there was a resurgence of the disease since the 80s. This disruption is due to coinfection with HIV/AIDS, disorganization of health systems and the emergence of bacteria resistant to anti-TB drugs. In this context, a better understanding of the movements and changes of circulating clones of tubercle bacilli would detect faster and more relevant emerging epidemics. The control and monitoring of the disease are essential means to fight against the worldwide spread of tuberculosis. Thus the TB and Mycobacteria unit of the Pasteur Institute of Guadeloupe (IPG) has developed a database of genotypic profiles for the study of global epidemiology of tuberculosis.In this thesis, we discuss the Bioinformatical methods that have been used for the management and development of the 6th version (SITVIT2) of this database of genotypes to better understand the evolution and global dissemination of the tubercle bacillus. The database also includes several molecular markers such as MIRU-VNTRs (mycobacterial interspersed repetitive units- variable number of tandem repeats) and Spoligotype43 allowing a better description and identification of the families of genotypic profiles of Mycobacterium tuberculosis complex. SITVIT2 database is constantly evolving, and it currently contains epidemiological information on 111,635 clinical isolates. This database is available online at the following address: http://www.pasteur-guadeloupe.fr:8081/SITVIT2/. We also developed a database named "SITVITBovis", which is dedicated to bovine tuberculosis. This database will be accessible at: http://www.pasteur-guadeloupe.fr:8081/SITVIT_Bovis/.Alongside the development and management of databases, this work was based on several epidemiological and phylogeographic studies correlating data on drug resistance or demographic characteristics (including sex, age, HIV status, and the origin of the patient). Our research initiative is thus focused to further improve in depth phylogenetic characterization of MTBC lineages, as well as the epidemiological analysis of circulating clones to generate evidence-based geographical mapping of predominant clinical isolates of tubercle bacilli causing the bulk of the disease both at country and regional level. Further superposition of these maps with socio-political, economical and demographical available through Geographic Information Systems (GIS) allows to have a precise view of prevailing disparities at the level of country or sub-region. This thesis represents an important collaboration with several researchers teams also working in the field of molecular epidemiology of tuberculosis.The long-term goal of this work is to further optimize the database structure, and sustain enriching it (including automation and ease of data entry). Optimum performance and accessibility of data in the database would reinforce efforts to control and surveillance of TB in the world.

http://www.theses.fr/2014AGUY0791/document